pheval 0.1.0__py3-none-any.whl → 0.2.0__py3-none-any.whl

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Files changed (42) hide show
  1. pheval/__init__.py +0 -5
  2. pheval/analyse/__init__.py +0 -0
  3. pheval/analyse/analysis.py +703 -0
  4. pheval/analyse/generate_plots.py +312 -0
  5. pheval/analyse/generate_summary_outputs.py +186 -0
  6. pheval/analyse/rank_stats.py +61 -0
  7. pheval/cli.py +22 -7
  8. pheval/cli_pheval.py +37 -12
  9. pheval/cli_pheval_utils.py +225 -8
  10. pheval/config_parser.py +36 -0
  11. pheval/constants.py +1 -0
  12. pheval/implementations/__init__.py +1 -3
  13. pheval/post_processing/__init__.py +0 -0
  14. pheval/post_processing/post_processing.py +210 -0
  15. pheval/prepare/__init__.py +0 -0
  16. pheval/prepare/create_noisy_phenopackets.py +173 -0
  17. pheval/prepare/create_spiked_vcf.py +366 -0
  18. pheval/prepare/custom_exceptions.py +47 -0
  19. pheval/prepare/update_phenopacket.py +53 -0
  20. pheval/resources/alternate_ouputs/CADA_results.txt +11 -0
  21. pheval/resources/alternate_ouputs/DeepPVP_results.txt +22 -0
  22. pheval/resources/alternate_ouputs/OVA_results.txt +11 -0
  23. pheval/resources/alternate_ouputs/Phen2Gene_results.json +814 -0
  24. pheval/resources/alternate_ouputs/Phenolyzer_results.txt +12 -0
  25. pheval/resources/alternate_ouputs/lirical_results.tsv +152 -0
  26. pheval/resources/alternate_ouputs/svanna_results.tsv +9 -0
  27. pheval/resources/hgnc_complete_set_2022-10-01.txt +43222 -0
  28. pheval/run_metadata.py +27 -0
  29. pheval/runners/runner.py +92 -11
  30. pheval/utils/__init__.py +0 -0
  31. pheval/utils/docs_gen.py +105 -0
  32. pheval/utils/docs_gen.sh +18 -0
  33. pheval/utils/file_utils.py +88 -0
  34. pheval/utils/phenopacket_utils.py +356 -0
  35. pheval/utils/semsim_utils.py +156 -0
  36. {pheval-0.1.0.dist-info → pheval-0.2.0.dist-info}/METADATA +12 -4
  37. pheval-0.2.0.dist-info/RECORD +41 -0
  38. {pheval-0.1.0.dist-info → pheval-0.2.0.dist-info}/WHEEL +1 -1
  39. pheval/utils.py +0 -7
  40. pheval-0.1.0.dist-info/RECORD +0 -13
  41. {pheval-0.1.0.dist-info → pheval-0.2.0.dist-info}/LICENSE +0 -0
  42. {pheval-0.1.0.dist-info → pheval-0.2.0.dist-info}/entry_points.txt +0 -0
pheval/resources/alternate_ouputs/Phenolyzer_results.txt ADDED
@@ -0,0 +1,12 @@
1
+ Rank Gene ID Score Status HaploinsufficiencyScore GeneIntoleranceScore
2
+ 1 PSEN1 5663 1 SeedGene 0.955 0.6962727058
3
+ 2 STIM1 6786 0.9852 SeedGene 0.206 0.6245576787
4
+ 3 PLA2G6 8398 0.9517 SeedGene 0.150 0.96915546119
5
+ 4 MAPT 4137 0.9491 SeedGene 0.245 0.0191082803
6
+ 5 VCP 7415 0.948 SeedGene 0 0.6993394669
7
+ 6 SQSTM1 8878 0.9465 SeedGene 0.829 0.651155933
8
+ 7 TREM2 54209 0.9357 SeedGene 0.039 0.2074781788
9
+ 8 GRN 2896 0.9141 SeedGene 0.103 0.7633875914
10
+ 9 CHMP2B 25978 0.8982 SeedGene 0.281 0.583569238
11
+ 10 C9ORF72 203228 0.8536 SeedGene 0.219 0.8045529606
12
+ 11 OPA3 80207 0.8536 SeedGene 0.115 0.2487615004